The Cellular Editor concept:

Parts / Organelles:

• Vesicle: Vesicles can be used to create vacuoles, peroxisomes, lysosomes, etc. The chemical inside can be determined as well as their size.
  
• Cytoskeleton: The Cytoskeleton can be used to create a preset shape for the cell and also to join organelles together. It can be used to create Endoplasmic Reticuli, Golgi Bodies, Cytostomes and Undilopodia such as Cilia, Flagella and Psuedopods. They can attach to almost everything including the cell membrane and modified for length. The cell has several default cytoskeleton.
  
• Motor Proteins: A special type of cytoskeleton that is used in flagella. This organelle / protein creates a propeller motion.
  
• Nucleus: Nuclei can be modified by size and placed in almost any fashion.
  
• Cisterna: Cisternae are disc-like organelles that can be attached together by Cytoskeleton to form Golgi Apparati and Endoplasmic Reticulum. They speed up the transfer of proteins across their surface.
  
• Thylakoid: Photosynthesizing component. Can be adjusted to vary in what type of photosynthesis (purple sulphur, oxygenic, etc.). As far as we know these only ever evolved once on Earth, so they should be pretty difficult to get.
  
• Polysacharride: Are thick ridged, wall-like components that can form a structure similar to a fence that can hold a cells structure. They can be used to create a Cell wall and form shells. The Thickness and Strength can be modified.
  
• Pilus: Pili are used to share DNA between cells. These are used for sexual reproduction.
  
• Cell Membrane: The Cell Membrane can be increased in length and modified in a properties window. The Cell Membrane can be specialised for cases such as mitochondrial cell membranes. The membrane can be extended and molded via cytoskeleton to create flagella and cilia.

The tools for mass modifications are similar to the tools for the OE, copy and paste parts.

Internalised symbiosis will be done via declaring prokaryote (without a nuclei) cells as existing inside the cell (this cannot be done with the in-gameplay editor and can only be added via engulfment in-game). The fitness calculations take into account the symbiotic organisms.

Reproduction will be handled via a fraction. This will determine the number of membrane nodes the parent wishes to give to the offspring. This number can go up to 1/2 (mitosis with sister cells). A cell's ability to reproduce is determined by the size of its membrane. Organelles (specifically nuclei and symbiotes) must be inside the daughter cell as it is split off, therefore the fraction can not be below the membrane size required to contain these organelles.

Cell movement uses three different methods: Undulation (like an Amoeba), Flagellation (via a flagella) and Cilia (cytoskeleton + short membrane sections).

• Undulation is the default movement pattern where speed is determined by cytoskeleton density and membrane plasticity, size and a high ratio of membrane to volume. It is slow and irregular.
  
• Flagellation results in a high speed cell which turns relatively slowly.
  
• Cilia is regular and of medium speed. It relies on large number of well place cilia.
  

The Cell Membrane can be modified for thickness, plasticity, porousness and certain proteins which increase efficiency in areas of cell activity.

I have uploaded a Proof-of-Concept Prototype, it is incomplete and now outdated:
Thrive - Cellular Editor, GXA - Prototype

Should methods of eating be included? For example:

• Taking the other cell's cytoplasm & membrane and adding it to your cells, basically absorbing.
  
• Enclosing another cell, encasing it in a bubble inside your cell which is filled with digestive juices.

There will probably be words for these methods, but I don't think I know them...

Also, what about Mitochondria, or some equivalent? They are important for our cells to work.

I have been unable to think of how to incorporate symbiosis... Any suggestions anyone?

Well I thought this little flash game had it pretty accurate. http://www.newgrounds.com/portal/view/541743 We could take a few hints if we want.

It's a good game, but i'm not sure if it plays like we want our cell stage to play.

I have edited the OP with a link to a Proof-of-Concept Prototype I have created for the Cellular Editor. It is incomplete though.

The Cytoskeleton is used to control the cell's shape by placing it in certain ways in the cell. Polysaccharides are also placed around the Cell Membrane to form a Cell Wall.

The Mouse Wheel is used to size the cytoskeleton and other organelles.

only other things to add are the golgi body, mitochondria, cytoplasm, and for the sake of plant/animal hybrids, add chloroplasts.

Those are accomplished by joining together multiple Cisternae with the Cytoskeleton. I still do not now how symbiosis will occur though.

Wow. Should have checked this post before I posted elsewhere.

Just got done with wondering whether we'd get our organelles a la carte.
Hmm...
I say we remember our "attachments" such as cilia, flagella, etc. Also, some bacteria encyst themselves, so if we had an organelle that did that, rather than a complicated ulterior method, that might work.

Symbiosis? Are you talking about with a larger organism? Because we'd probably just make the microbe to do whatever function in the editor, then "incorporate" it into the creature/plant/coral or whatever.
Mitochondria might be a good place if people want to look at evolutionary/gameplay data, as in real life it provides power to the cell and stores a copy of maternal (mitochondrial) DNA.

Also, how are we getting Chloroplasts out of cysternae? They're pretty different ... I mean, the shapes are the same, and when adding Chloroplasts we'd really be adding a region stuffed with the things, but they're so different in function. I'd just put in the option "add chloroplasts" and watch the cell turn green. Or, another color, provided that we give them chromatophores.

I think that we can bend and stretch the cell's shape all we want, but it's optional organelles and other "instructions" that are going to make it different from all the other single-celled blobs out there.